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- EMDB-18435: 420A Vipp1 H1-6 helical tubes -

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Basic information

Entry
Database: EMDB / ID: EMD-18435
Title420A Vipp1 H1-6 helical tubes
Map data
Sample
  • Complex: Vipp1 H1-6
    • Protein or peptide: Membrane-associated protein Vipp1
Keywordsmembrane remodeling / membrane tubulation / LIPID BINDING PROTEIN
Function / homologyPspA/IM30 / PspA/IM30 family / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsJunglas B / Sachse C
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SA 1882/6-1 Germany
German Research Foundation (DFG)SCHN 690/16-1 Germany
Citation
Journal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies.
Authors: Benedikt Junglas / David Kartte / Mirka Kutzner / Nadja Hellmann / Ilona Ritter / Dirk Schneider / Carsten Sachse /
Abstract: Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting ...Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting complexes required for transport III superfamily, it is still unknown how Vipp1 remodels membranes. Here, we present cryo-electron microscopy structures of Synechocystis Vipp1 interacting with membranes: seven structures of helical and stacked-ring assemblies at 5-7-Å resolution engulfing membranes and three carpet structures covering lipid vesicles at ~20-Å resolution using subtomogram averaging. By analyzing ten structures of N-terminally truncated Vipp1, we show that helix α0 is essential for membrane tubulation and forms the membrane-anchoring domain of Vipp1. Lastly, using a conformation-restrained Vipp1 mutant, we reduced the structural plasticity of Vipp1 and determined two structures of Vipp1 at 3.0-Å resolution, resolving the molecular details of membrane-anchoring and intersubunit contacts of helix α0. Our data reveal membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.
#1: Journal: Biorxiv / Year: 2024
Title: Structural basis for Vipp1 membrane binding: From loose coats and carpets to ring and rod assemblies
Authors: Junglas B / Kartte D / Kutzner M / Hellmann N / Ritter I / Schneider D / Sachse C
History
DepositionSep 11, 2023-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18435.png

Downloads & links

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Map

FileDownload / File: emd_18435.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 350 pix.
= 840. Å		2.4 Å/pix.
x 350 pix.
= 840. Å		2.4 Å/pix.
x 350 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.267
Minimum - Maximum-0.24054539 - 0.88927907
Average (Standard dev.)0.0050122794 (±0.04196259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 840.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18435_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18435_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vipp1 H1-6

EntireName: Vipp1 H1-6
Components
  • Complex: Vipp1 H1-6
    • Protein or peptide: Membrane-associated protein Vipp1

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Supramolecule #1: Vipp1 H1-6

SupramoleculeName: Vipp1 H1-6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Membrane-associated protein Vipp1

MacromoleculeName: Membrane-associated protein Vipp1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 21.060562 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DPEKVLEQAV IDMQEDLVQL RQAVARTIAE EKRTEQRLNQ DTQEAKKWED RAKLALTNGE ENLAREALAR KKSLTDTAAA YQTQLAQQR TMSENLRRNL AALEAKISEA KTKKNMLQAR AKAAKANAEL QQTLGGLGTS SATSAFERME NKVLDMEATS Q AAGELAGF ...String:
DPEKVLEQAV IDMQEDLVQL RQAVARTIAE EKRTEQRLNQ DTQEAKKWED RAKLALTNGE ENLAREALAR KKSLTDTAAA YQTQLAQQR TMSENLRRNL AALEAKISEA KTKKNMLQAR AKAAKANAEL QQTLGGLGTS SATSAFERME NKVLDMEATS Q AAGELAGF GIENQFAQLE ASSGVEDELA ALKA

UniProtKB: Membrane-associated protein Vipp1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.73 Å
Applied symmetry - Helical parameters - Δ&Phi: 82 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49285
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7o3w

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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